Analysis Workflow

SimBiology® lets you analyze models of dynamic systems. For instance, you can simulate various biological systems such as signaling pathways and explore what-if hypotheses. You can investigate system dynamics and guide experimentation using parameter sweeps and sensitivity analysis. Various dosing regimens can be evaluated to assess different combination therapies. In addition, you can use experimental time course data to estimate model parameters using nonlinear regression or mixed-effects techniques.

To perform these analyses, the SimBiology desktop provides built-in MATLAB® scripts with a user interface called tasks. Each task is open and displayed in the task editor, where you can configure the task’s settings such as specifying how long the simulation runs. The desktop automatically checks for errors and warnings as you configure the task and flags any issues using message indicators.

As a task is running, it displays a plot that shows the values of model quantities over time. The plot is updated live as the model is simulated. You can also add experimental data to the plot to compare with simulation results.

The desktop provides interactive model exploration tools that let you vary parameter values, initial conditions, and dosing schedules. For instance, you can simulate the model and interactively vary the value of a parameter of interest. The live plot automatically updates for the change, and you can check the plot to see if the simulation result using the new parameter value is close to experimental data. Then you can use the new value as an initial estimate when you perform parameter estimation.

Once the task finishes, you can visualize the results using different MATLAB plots. The desktop provides a default set of plots and selects the plots that are appropriate for the specific task being run. You can add additional plots to gain more insight into your results. You can export the results to MATLAB workspace or share with others by saving the results in a MAT or Excel® file.

The desktop provides the equivalent MATLAB script for each task. You can use these scripts as templates and modify them as necessary. For instance, you can modify the parameter scan task for more flexible sampling options using other MATLAB functions. You can write such scripts from within the task editor by creating a custom task, which is saved with the project.

You can also create standalone applications for model distribution and simulation. Suppose you want to share your model and analysis with non-modelers using a simple standalone application. You, as a modeler, can hide the details of the model and decide what model information to expose to other non-modelers. With the desktop you can build such an application that end users can use to vary model parameters, modify dosing schedules, visualize the dynamics of key response variables, and save the results. For details, see Deployment.

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